The Join Features tool in ArcGIS Online has approximately 500 fields limit.

Additional Information

Workaround

1. Open the .csv file in Microsoft Excel.
2. Manually pare down the number of fields to 500 or less.
3. Open a new map in ArcGIS Online.
4. Click Add > Add Layer from File.
5. Add a zipped polygon shapefile and a .csv file with 600 fields or more.
6. Click Analysis > Summarize Data > Join Features.
7. Select the .csv file as a target layer, and polygon shapefile as a layer to join to the target layer.
8. Select the Completely within option under Choose a spatial relationship.
9. Click Run Analysis.
10. The Join Features tool runs as expected.

Steps to Reproduce